How does enzyme work?
Enzymes are biomolecules and they speed up reactions by decreasing the rate of a chemical reaction. Enzymes will not alter reaction equilibrium but decrease rate of the chemical reaction by decreasing the free energy of activation. Enzymes work by facilitating and accelerating chemical reactions in living organisms. They achieve this by lowering the activation energy required for a reaction to occur, making it easier for the reaction to proceed. To know more please watch the below-embedded video.
Mechanism of enzyme action
There are two theories or models or hypotheses for the mechanism of enzyme action. The first theory proposed by Emil Fisher, known as lock and key model or rigid template model or Fisher model and the second one is the induced fit model or hand-in-glove model or Koshland model proposed by Daniel E Koshland.
The mechanism of enzyme action involves several steps and interactions between the enzyme, substrate, and catalytic residues within the active site. The general mechanism can be described as follows:
- Substrate Binding: The enzyme and substrate molecules come together, and the substrate binds to the enzyme’s active site through non-covalent interactions such as hydrogen bonding, electrostatic interactions, and hydrophobic interactions. This binding is specific and relies on the complementary shapes and chemical properties of the active site and substrate.
- Formation of the Enzyme-Substrate Complex: The binding of the substrate to the enzyme’s active site leads to the formation of the enzyme-substrate complex. This complex brings the substrate molecules in close proximity, facilitating the reaction.
- Transition State Formation: Within the active site, the enzyme interacts with the bound substrate to stabilize the transition state. The transition state is the high-energy intermediate state that must be reached for the reaction to occur. The enzyme achieves this by precisely positioning the substrate and using catalytic residues within the active site to facilitate the necessary chemical transformations.
- Catalysis: The enzyme catalyzes the conversion of the substrate into the product(s) by lowering the activation energy required for the reaction to proceed. Enzymes can employ various catalytic strategies:
- Acid-Base Catalysis: The enzyme donates or accepts protons, altering the substrate’s chemical properties and facilitating the reaction.
- Covalent Catalysis: The enzyme forms a temporary covalent bond with the substrate, stabilizing the transition state and promoting the reaction.
- Metal Ion Catalysis: The enzyme utilizes metal ions to facilitate the reaction by coordinating with the substrate or participating in redox reactions.
- Proximity and Orientation Effects: The enzyme brings the reactive groups of the substrate into close proximity and proper orientation, increasing the likelihood of a favorable reaction.
- Product Formation and Release: The catalytic action of the enzyme leads to the conversion of the substrate into the product(s). The products have different chemical properties and are no longer tightly bound to the enzyme. The enzyme releases the products, and it can then bind to another substrate molecule to repeat the process.
Throughout the reaction, enzymes act as catalysts, enabling the reaction to occur rapidly and efficiently. They do not undergo any permanent changes or get consumed in the process, allowing them to participate in multiple rounds of substrate conversion. Enzyme activity is influenced by factors such as substrate concentration, temperature, pH, and the presence of inhibitors or activators, which can modulate the rate of the reaction.
The specific details of enzyme mechanisms vary depending on the enzyme and the reaction it catalyzes. The active site structure, amino acid residues, and cofactors or coenzymes associated with the enzyme all contribute to its unique catalytic properties and mechanisms of action.
The active site of an enzyme
The active site of an enzyme is a specific region or pocket on the enzyme’s surface where the catalytic activity takes place. It is a highly specialized and structurally defined area that allows the enzyme to bind to its substrate(s) and facilitate the catalytic reaction. The active site is typically composed of amino acid residues from different parts of the enzyme’s polypeptide chain.
Key features of the active site include:
- Binding Site: The active site contains specific amino acid residues that interact with the substrate through various non-covalent interactions, such as hydrogen bonding, electrostatic interactions, and hydrophobic interactions. These interactions provide specificity and ensure that only the correct substrate(s) can bind to the active site.
- Catalytic Residues: Within the active site, certain amino acid residues play a direct role in the catalytic activity of the enzyme. These residues can act as acid-base catalysts, nucleophiles, or other functional groups that participate in the chemical reaction. They facilitate the conversion of the substrate(s) into product(s) by stabilizing transition states, facilitating bond rearrangements, or providing the necessary environment for the reaction to occur.
- Substrate Specificity Determinants: The active site structure and composition contribute to the enzyme’s substrate specificity. The active site residues can form a complementary shape and chemical environment that is specific to the substrate(s) with which the enzyme interacts. This ensures that the enzyme selectively binds to its target substrate(s) and excludes other molecules that do not fit the active site.
- Induced Fit: The active site is not rigid but can undergo conformational changes upon substrate binding. This phenomenon, known as induced fit, allows the enzyme to adjust its shape to better accommodate and interact with the substrate(s). The binding of the substrate induces conformational changes in the active site that optimize the interactions between the enzyme and the substrate.
The precise arrangement and composition of the active site determine the enzyme’s specificity, efficiency, and regulation. Changes in the active site structure or amino acid residues can affect enzyme activity and specificity. Additionally, factors such as pH, temperature, and the presence of cofactors or coenzymes can influence the shape and function of the active site.
Understanding the structure and function of the active site is essential for studying enzyme kinetics, designing enzyme inhibitors or activators, and elucidating the molecular mechanisms of enzyme-catalyzed reactions. Please watch below embedded video to know more about the active site of an enzyme.
Cofactors and Coenzymes
If you take enzyme, it is a protein, almost all enzymes are proteins except ribozyme and this protein part of the enzyme is called apoenzyme. Several enzymes apart from being a protein, also possess a non-protein component. So, such nonprotein components are called cofactors. So, cofactors are non-protein components. So, this non-protein component of enzyme, we can call it as prosthetic groups. So, now we have an apoenzyme and we have prosthetic groups. So together apoenzyme and prosthetic group, we can call it as a holoenzyme. So, the prosthetic groups are collectively called as cofactors and these cofactors could be coenzymes or metal ions. Coenzymes are also cofactors even metal ions are also cofactors. Usually, these cofactors enhance enzyme-catalyzed reactions. So, usually, coenzymes are organic components. whereas metal ions are inorganic. To understand further please watch below embedded video.